Citromicrobium bathyomarinum is a bacteriochlorophyll a-containing aerobic anoxygenic phototrophic bacterium. Here, we report the draft genome sequence of C. bathyomarinum JL354, which was the first C. bathyomarinum strain isolated from a euphotic marine environment. The JL354 genome sequence reveals, for the first time, the coexistence of two different photosynthetic operons in a single strain.